A novel chemical ontology based on chemical functional groups automatically, objectively assigned by a computer program, was developed to categorize small molecules. It has been applied to PubChem and the small molecule interaction database to demonstrate its utility as a basic pharmacophore search system. Molecules can be compared using a semantic similarity score based on functional group assignments rather than 3D shape, which succeeds in identifying small molecules known to bind a common binding site. This ontology will serve as a powerful tool for searching chemical databases and identifying key functional groups responsible for biological activities.
Description
CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules
%0 Journal Article
%1 Feldman2005ChemicalOntology
%A Feldman, Howard J.
%A Dumontier, Michel
%A Ling, Susan
%A Haider, Norbert
%A Hogue, Christopher W.V.
%D 2005
%J \FEBS\ Letters
%K chemoinformatics functional-groups ontology
%N 21
%P 4685 - 4691
%R http://dx.doi.org/10.1016/j.febslet.2005.07.039
%T CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules
%U http://www.sciencedirect.com/science/article/pii/S001457930500894X
%V 579
%X A novel chemical ontology based on chemical functional groups automatically, objectively assigned by a computer program, was developed to categorize small molecules. It has been applied to PubChem and the small molecule interaction database to demonstrate its utility as a basic pharmacophore search system. Molecules can be compared using a semantic similarity score based on functional group assignments rather than 3D shape, which succeeds in identifying small molecules known to bind a common binding site. This ontology will serve as a powerful tool for searching chemical databases and identifying key functional groups responsible for biological activities.
@article{Feldman2005ChemicalOntology,
abstract = {A novel chemical ontology based on chemical functional groups automatically, objectively assigned by a computer program, was developed to categorize small molecules. It has been applied to PubChem and the small molecule interaction database to demonstrate its utility as a basic pharmacophore search system. Molecules can be compared using a semantic similarity score based on functional group assignments rather than 3D shape, which succeeds in identifying small molecules known to bind a common binding site. This ontology will serve as a powerful tool for searching chemical databases and identifying key functional groups responsible for biological activities. },
added-at = {2016-08-19T21:18:31.000+0200},
author = {Feldman, Howard J. and Dumontier, Michel and Ling, Susan and Haider, Norbert and Hogue, Christopher W.V.},
biburl = {https://www.bibsonomy.org/bibtex/2898d684cef472b824b47ac0ca310871c/salotz},
description = {CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules},
doi = {http://dx.doi.org/10.1016/j.febslet.2005.07.039},
interhash = {d671f28f00a7da2a5c31e091eecfa072},
intrahash = {898d684cef472b824b47ac0ca310871c},
issn = {0014-5793},
journal = {\{FEBS\} Letters },
keywords = {chemoinformatics functional-groups ontology},
number = 21,
pages = {4685 - 4691},
timestamp = {2016-08-19T21:18:31.000+0200},
title = {CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules },
url = {http://www.sciencedirect.com/science/article/pii/S001457930500894X},
volume = 579,
year = 2005
}